A Matter of Choice
by JohnnyStyle
Summary: The choices I would of liked to have made at the end of ME3. A triple shot featuring featuring chapters for my renagade and paragon Shepards. The third is about what would have happened if some one had calibrated the crucible properly. Rated M for Mild Violence, coarse lanuage, adult themes, sexual refernces and still managing to get in some Liara goodness.
1. Negotiations at the end of the world

**Negotiations at the end of the world**

"So what you're saying is I can either wipe out a friendly synthetic species at the same time I destroy the reapers, becoming the one doing the Indoctrinating or force everyone onto the same evolutionary path?"

"They will diverge eventually, but yes."

"And all these options cause the destruction of the mass relays?"

"That can be the only outcome of using the crucible yes," replied the entity.

"All horrible choices," Jane Daria Shepard said. "Especially if I make them right now."

"Nether the less you must make the choice."

"And leave the quarians and turians stranded without any food? The krogan without a way to get home to their new families? And even the Asari with a trip that would take them generations?"

"You must make a choice."

"Then I chose none of these three," Jane Daria Shepard stated.

"But these are what the crucible has unlocked in order to end the cycle."

"Then think of me as a second crucible presenting more solutions, more options," Shepard explained as she sat on the ground and put down her pistol. "Negotiation is what I offer, a solution I believe you...catalyst, may not have considered."

"Impossible."

"That is because you're operating under the false assumption that synthetic and organic life cannot coexist."

"But the option for coexistence is open, chose synthesis."

"I won't force that on beings who want to remain one hundred percent of either," Jane Daria sighed. "I have no right to make that choice for anyone."

"But you are the one who stands here."

"Like you," Shepard grunted. "That's part of the problem, the decision to perpetuate the cycle shouldn't have been in a single being's hands."

"The cycle would continue to a true total galactic extinction event without reaper intervention," the catalyst said. "I'm sure your prothean has told you of his own people's encounter with synthetic life?"

"Yes," Shepard admitted. "But the geth had already broken that. They did it at the end of their morning war, They did it by welcoming the Quarians home to Rannoch."

"Only due to your intervention."

"And your intervention forced the geth into conflict they didn't want there by forcing our cycle into you limited vision," Shepard bit back. "I wonder how many species, organics and synthetic, you have forced into war like you did the rachni."

"That was necessary."

"I suppose that's what was said when the first reaper was constructed," Shepard sighed. "I don't buy your explanation by the way."

"The reaper created at the height of a civilisation will not go extinct, will not fade and will not be destroyed by its own creations."

"And you destroy that civilisation, it's people in the process," Shepard said. "Everything it was is lost. What gave you the right to decide the creation of synthetic live was the height of civilisation anyway?"

"Chose!"

"First let my forces withdraw to the their home planets and colonies," Shepard said.

"Acceptable," The catalyst said.

"Second I want Harbinger tried for war crimes."

"Impossible."

"Listen," Jane Daria Shepard said. "Harbinger raped my people, I believe I will find countless witnesses to verify he did the same to theirs. I won't destroy the reapers, they could teach us much about galactic history that has been lost and could be valuable members of galactic society. But Harbinger must be held accountable for his crimes no matter what different moral standard the reapers use."

* * *

"In the end peace was made," the grandfather said to his grandchild. "The crucible features to enslave or destroy the reapers were switched off. The synthesis feature was adapted for use for individual conversion."

"And the Joker and the AI were the first to use it," the child interjected.

"Yes and they founded our planet."

"But grandfather what happened to the Shepard?"

"That has been lost," the grandfather said. "It all happened so long ago my sweet."

"Well the Glyph said she was born in space," the child reasoned. "Perhaps she and the Sky Goddess she loved, the one who liked to dug up planets looking for prothean stuff, are still out there."

"Having their eternal rest near some uncharted star?"

"Don't be silly, they're just hiding," the child said. "One day I'll go to the stars. I'll find other glyphs and restore the corrupted data."

"Then we'll know the whole truth?"

"You bet grandpa," the child replied. "Just like Shepard and her friends when they found that beacon."


	2. The Power of Friendship

**The Power of Friendships**

"Those choices suck," Xandi Shepard spat.

"Those are what the crucible has opened."

"Then you leave me no choice," Shepard smirked. "I was hoping it would come to this."

"What do you mean?" the catalyst construct asked.

"Ranchi please inform the fleets that phase three is go."

"What!"

"You really thought we wouldn't be wary of gifts from the past after we learnt the truth of the mass relays? Of the citadel?"

"You can end the reaper cycle right now!" the catalyst screamed.

"I am ending it," Shepard smirked again. "On my terms."

"Impossible."

"My friends are going to show you it isn't."

Shepard tilted her head to one side as if listening to something. She then touched her hand to her ear.

"Admiral Hackett?"

"We read you commander."

"Deploy the elcor and the bloodpack."

On the surface elcor outfitted with heavy weapons, and protected by vorcha from reaper ground troops, took aim. Suddenly hundreds of reaper destroyers were dead. The elcor had been patient and discovered exactly where to strike. Their Vorcha escorts viscously cleaned up the remain ground forces.

"Rannoch fleet," Shepard smiled. "one sovereign class at a time. Alliance fleet, Turain fleet protect their flanks. Crucible freighters deploy our remain krogan and Rachni ground troops to the points of heavy fighting. Asari and citadel forces blockade the relay."

Soon space around the citadel and crucible was filled with explosions. More reapers were being destroyed than ships of the combined military force. Harbinger made a break for the Charon relay. Soon the reaper was tumbling into the Jovian gravity well in pieces. The Destiny Ascension had broken ranks to attack and Shepard couldn't blame them. Upon their return to the relay they trapped some destroyers in a pincer movement. As the reaper forces dwindled some tried to flee using conventional FTL only to be met by the remnants of the batarian fleet and their own ends. Shepard had told Balak to not allow any reaper an escape.

"Give up this foolishness," The catalyst said.

"But I'm winning," Shepard said.

"Chose an action that the crucible as opened before you realise the futility of your attack. Just ask your Prothean about it."

"The Protheans who fought you long after you thought them harvested?"

"They all still died before they could really help you," the catalyst taunted. "Leaving you only one soldier who didn't complete his mission."

"Still you made mistake after mistake," Shepard said. "After mistake until it culminated in your largest one."

"What failing to control the Illusive man enough to have him control you."

"No, you fucked with Aria," Shepard said. "One rule in most parts of the galaxy this cycle. You don't fuck with Aria. Even I'm not that stupid and I've been known to run towards reapers."

"I'm on the citadel," came Aria's voice from Shepard's comm.

"You better recall your ground troops to protect your core systems," Shepard smirked. "I'm out of here, Joker come pick me up."

She focused her biotics and leapt away from the council tower. Right into the Normandy's shuttle bay and the waiting arms of Liara T'soni.

* * *

"Next Palaven was freed, rapidly followed by Tuchunka, Rannoch, even the Batarian's regained their home world and then finally..."

"The Shepard returned her wife's home world to the light," the child said. "It was on the day the volus slew the last of the great reapers and earned their place on the council's fifth seat."

"Indeed my sweet," the grandfather said. "Of course there were still many battles but they were of no importance compared to the new happy memories forged by the new families."

"Like the Shepard and her children digging up that park on Thessia?"

"Yes," the man said. "Or the Joker and the AI discovering this planet and founding our colony."

"Is it true the Shepard could fell a reaper destroyer with one punch?"

"What does the glyph tell you?"

"That she was a powerful biotic and she must have been flawed as her wife questioned her judgement sometimes."

"Perhaps we'll find out more when Ambassador platform prime 278 opens that time capsule the Normandy crew left in the care of the geth?"

"Maybe," the child replies. "One day I'll travel from star to star and protect the galaxy like the Shepard did and then maybe one day people will wonder about me."

"I'm sure they will," the grandfather said. "So what do you think think happened to the Shepard?"

"She's is buried here on planet Kaiden of course with the rest of her family," the child replied with belief. "Awaiting future archaeologists to find exactly where."


	3. Correctly Calibrated

**Correctly Calibrated**

**Full Paragon**

"Oh I see the problem," Shepard said to herself as she cast herself into the stream that** wo**uld unite organic and synthetic life. "It's not calibrated properly."

She reached out with her conciousness. There, not as good as Garrus, but enough to transmit the energy without destroying the mass relays. In fact with a bit of refinement. Her mind, her soul touched, every living thing within the galaxy. She made her offer some asked for time to think about it, some asked to be left as they were and some accepted straight away. She touched the keepers and asked them one last favour before she set them free. They built a smaller devices for those that wanted to weigh their options first. The insect like aliens were set free. Some decided to remain, others began to make plans to travel to parts unknown.

That done, it was now only a matter of form. Yes that would do for her and many of the her friends decided the same. She was glad that the rest of the galaxy chose a multitude of different ideas and got really creative. It was done and the new Shepard flew out of the stream and danced through space alongside the Normandy. Soon she was joined by Liara, Traynor, Garrus and Tali. Joker and EDI remained on board eager to see if the gift of synthesis had made being physically intimate a less delicate affair.

_So what now _Liara asked her mouth moved with the words but her companions heard it as a thought.

_I was thinking Ilos _Shepard grinned

_First lets just enjoy the show _Traynor suggested

Indeed it was a beautiful sight as the ground forces came up to join them either in ships or now under their own power. Some of the Reapers were quietly leaving while others decided they would like to join the rest of the galaxy. Tali removed her mask as she no longer needed it.

_Guys I think I can feel the solar wind _she said as she removed some more layers of her suit. Soon word came that Krogan females who had accepted Shepard's gift had began coming in through the relay to reunite with their males. Saturn's rings became a dance floor as they shared their tender moments. The Williams sisters had an impromptu reunion at Tranquillity base. And even Javik decided to postpone his atonement to the men he lost so long ago so he could see the new wonders of the galaxy. After a week the party in the Sol system began to wind down and the crew of the Normandy decided now was the time to go their separate ways. Traynor and Allers had decided to document the new civilisation for prosperity. Their first stop was a rebuilding Thessia. Everyone else suspect the next time they saw they pair they would probably have married. Garrus and Tali decided to go build that house on Rannoch together, stopping by Palaven to check on Garrus's family on the way. Joker and EDI received permission to point the Normandy towards unexplored space and left with a crew consisting of people from every space faring species, and one very polite yahg. Ash and Vega decided to help the millitaries move over to a more policing role. Jack returned with her students to Grissom academy, with Miranda and Oriana in tow. Kasumi planned some new capers and was vague about were she was headed. Grunt, Wrex and Jacob all returned to their new families. Samara returned to the Ardat-Yakshi monastery to mourn her two deceased daughters and celebrate her remaining one could now have a real life thanks to the changes synthesis had made . A few of the other crew decided just to hang around earth and help with the rebuilding. Finally Shepard and Liara used the Charon relay to leave the Sol System.

_Even more exciting then when we drove the Mako through the conduit _Shepard remarked after the first jump.

Eventually they did end up on Ilos. They had taken the time to visit the graves of fallen friends and lament that they couldn't share this new era but rejoice that their sacrifices had not been in vain. After Ilos who knew what was next, the galaxy after all was an amazing place full of possibilities.

* * *

**Selfish Renegade**

Through the pain Shepard realised something.

"Damn thing isn't calibrated properly," she swore to herself. "Should have gotten Garrus to give this thing the once over."

She gritted her teeth and willed the calibration to happen. It wasn't quite the epic tweak Garrus could give the guns but it was enough to stop the energy release from destroying the relay network. She then reached out. The reapers we're now hers. It was time to do something about them. She turned their weapons on each other. When she got bored of that she bid them to tear each other apart limb from limb. Some she sent into the black hole beyond the omega 4 relay. Others into the hearts of stars. Anyway she could think of that might kill a reaper she tried. Soon there was only on left. A single destroyer. She smiled as she imagined the throngs of the galaxy cheering the destruction. She finally let herself become truly one with that last reaper. Her frail human and cybernetic body was gone. Her new body was the only one of its kind now in existence.

She adjusted the broadcast equipment so that it wouldn't send messages in that reaper voice that always kind of got on her nerves.

"This is Commander Shepard," she said. "I am in control of the last surviving reaper, we've won."

"I'll leave the rebuilding to everyone else," she said after the cheers died down. "And honestly you probably won't ever hear from me again."

"Why is that Shepard?" Admiral Hackett asked.

"I'm resigning," Shepard said. "I've just got to pick up my future wife and ask an AI about fabricating a realistic recreation of my physical body."

"What's that mean?" Liara asked worried over the communications channel everyone was listening to.

"Umm..." Shepard muttered. "I sort of need it to continue the physical aspect of our relationship."

"And why is that?" Liara asked in a tone that indicate this would go very badly for Shepard if she answered wrong.

"I'm kinda a reaper now."

"What!"

"Liara please don't be mad. I know what they did to your mother but I've turned off all indoctrination signals. I'm in the process of deleting all information about the process and I'm setting all weapons controls to only respond to your commands. And I'm just pretty sure this is the only way I can live as long as you do."

"When I come aboard you better know we will be having a nice long talk," Liara growled. "And consider yourself lucky I just might have plans for a robotic replica of you in the files from my other job."

A few months later Shepard and Liara were preparing to set out.

"Have you forgiven me yet?" Shepard asked through the robotic body she could remotely operate from the true seat of her conciousness.

"Almost," Liara admitted. "But first to Ilos."

"Of course mistress."


End file.
